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Yorodumi- PDB-9z9e: Structure of FabS1CE2_ER-3c in complex with the extracellular reg... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9z9e | |||||||||
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| Title | Structure of FabS1CE2_ER-3c in complex with the extracellular region of EGFR | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / epidermal growth factor receptor / high-affinity antibody / domain 3 / epidermal growth factor / inhibition | |||||||||
| Function / homology | Function and homology informationmultivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / epidermal growth factor binding / regulation of peptidyl-tyrosine phosphorylation / response to UV-A ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / epidermal growth factor binding / regulation of peptidyl-tyrosine phosphorylation / response to UV-A / ubiquitin-dependent endocytosis / PLCG1 events in ERBB2 signaling / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / ERBB2-EGFR signaling pathway / Signaling by EGFR / eyelid development in camera-type eye / intracellular vesicle / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Developmental Lineage of Mammary Gland Myoepithelial Cells / protein insertion into membrane / protein tyrosine kinase activator activity / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / negative regulation of epidermal growth factor receptor signaling pathway / PI3K events in ERBB2 signaling / hair follicle development / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / GAB1 signalosome / salivary gland morphogenesis / xenobiotic transport / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / epithelial cell proliferation / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / basal plasma membrane / ossification / cellular response to epidermal growth factor stimulus / positive regulation of DNA replication / positive regulation of epithelial cell proliferation / positive regulation of DNA repair / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / cellular response to estradiol stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to amino acid stimulus / sperm end piece / NOTCH3 Activation and Transmission of Signal to the Nucleus / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / EGFR downregulation / receptor protein-tyrosine kinase / Constitutive Signaling by EGFRvIII / negative regulation of protein catabolic process / cell-cell adhesion / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of protein phosphorylation / positive regulation of miRNA transcription / positive regulation of fibroblast proliferation / cell morphogenesis / epidermal growth factor receptor signaling pathway / ruffle membrane / kinase binding / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / neuron differentiation / HCMV Early Events / actin filament binding / cell junction / transmembrane signaling receptor activity / PIP3 activates AKT signaling / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / sperm principal piece / virus receptor activity / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / double-stranded DNA binding / sperm midpiece / early endosome membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Singer, A.U. / Mallette, E. / Bruce, H.A. / Blazer, L.L. / Adams, J.J. / Suits, M.D.L. / Sidhu, S.S. | |||||||||
| Funding support | Canada, 2items
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Citation | Journal: Protein Sci. / Year: 2026Title: Dual targeting of inhibitory EGFR epitopes with synthetic antibodies in therapeutic-resistant cancers. Authors: Adams, J.J. / Mallette, E. / London, M. / Liang, R.J. / van Dyk, D. / Pavlovic, Z. / Pot, I. / Geyer, C.R. / Bruce, H.A. / Blazer, L.L. / Hokanson, C.A. / Suits, M.D.L. / Singer, A.U. / Sidhu, S.S. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9z9e.cif.gz | 485.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9z9e.ent.gz | 351.5 KB | Display | PDB format |
| PDBx/mmJSON format | 9z9e.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/9z9e ftp://data.pdbj.org/pub/pdb/validation_reports/z9/9z9e | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 9z9fC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-Protein , 1 types, 1 molecules A
| #1: Protein | Mass: 69133.773 Da / Num. of mol.: 1 / Mutation: residues 25-645 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Plasmid: PSCSTADetails (production host): N-terminal trypsinogen-2 signal peptide and a C-terminal thrombin cleavage site followed by a hexahistidine tag Cell line (production host): Expi293 / Production host: Homo sapiens (human)References: UniProt: P00533, receptor protein-tyrosine kinase |
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-Antibody , 2 types, 2 molecules DE
| #2: Antibody | Mass: 24696.559 Da / Num. of mol.: 1 / Mutation: K127Q and E158G Source method: isolated from a genetically manipulated source Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY. Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSDCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
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| #3: Antibody | Mass: 23198.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
-Sugars , 3 types, 6 molecules 
| #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 8 types, 285 molecules 














| #7: Chemical | ChemComp-SCN / #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-NA / #10: Chemical | #11: Chemical | ChemComp-PEG / #12: Chemical | ChemComp-PGE / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.04 % |
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| Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2M potassium thiocyanate, 20% PEG3350, cryoprotected with this buffer plus 30% ethylene glycol Temp details: room temperature |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979346 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2025 / Details: mirrors |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.979346 Å / Relative weight: 1 |
| Reflection | Resolution: 2.4→43.112 Å / Num. obs: 66379 / % possible obs: 95.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 40.33 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.106 / Rrim(I) all: 0.168 / Net I/σ(I): 7.9 |
| Reflection shell | Resolution: 2.4→2.443 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3445 / CC1/2: 0.364 / Rpim(I) all: 1.029 / Rrim(I) all: 1.619 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.11 Å / SU ML: 0.3167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2485 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 58.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.4→43.11 Å
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
Canada, 2items
Citation
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